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Can sequence determine function?
John A Gerlt, Patricia C Babbitt
Genome Biol. 2000; 1(5): reviews0005.1–reviews0005.10. Published online 2000 November 8.
PMCID:
PMC138884
Abstract Full Text PDF–469K
 Is Cited by the Following 21 Articles in this Archive:
Mycobacterium tuberculosis Rv2419c, the missing glucosyl-3-phosphoglycerate phosphatase for the second step in methylglucose lipopolysaccharide biosynthesis
Vítor Mendes, Ana Maranha, Susana Alarico, Milton S. da Costa, Nuno Empadinhas
Sci Rep. 2011; 1: 177. Published online 2011 November 30. doi: 10.1038/srep00177
PMCID:
PMC3240985
Abstract Full Text PDF–2.4M
Searching the protein structure database for ligand-binding site similarities using CPASS v.2
Robert Powers, Jennifer C Copeland, Jaime L Stark, Adam Caprez, Ashu Guru, David Swanson
BMC Res Notes. 2011; 4: 17. Published online 2011 January 26. doi: 10.1186/1756-0500-4-17
PMCID:
PMC3057182
Abstract Full Text PDF–8.0M
Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors
Adrian Schröder, Johannes Eichner, Jochen Supper, Jonas Eichner, Dierk Wanke, Carsten Henneges, Andreas Zell
PLoS One. 2010; 5(11): e13876. Published online 2010 November 30. doi: 10.1371/journal.pone.0013876
PMCID:
PMC2994704
Abstract Full Text PDF–1.3M Supplementary Material
Knowledge-based annotation of small molecule binding sites in proteins
Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko, Thomas Madej
BMC Bioinformatics. 2010; 11: 365. Published online 2010 July 1. doi: 10.1186/1471-2105-11-365
PMCID:
PMC2909224
Abstract Full Text PDF–1.9M Supplementary Material
A Comprehensive Analysis of Gene Expression Evolution Between Humans and Mice
Yupeng Wang, Romdhane Rekaya
Evol Bioinform Online. 2009; 5: 81–90. Published online 2009 July 6.
PMCID:
PMC2747126
Abstract Full Text PDF–568K
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning
Adrian K Arakaki, Ying Huang, Jeffrey Skolnick
BMC Bioinformatics. 2009; 10: 107. Published online 2009 April 13. doi: 10.1186/1471-2105-10-107
PMCID:
PMC2670841
Abstract Full Text PDF–334K Supplementary Material
FINDSITE: a combined evolution/structure-based approach to protein function prediction
Jeffrey Skolnick, Michal Brylinski
Brief Bioinform. 2009 July; 10(4): 378–391. Published online 2009 March 26. doi: 10.1093/bib/bbp017
PMCID:
PMC2691936
Abstract Full Text PDF–475K
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Gaëlle Lelandais, Véronique Tanty, Colette Geneix, Catherine Etchebest, Claude Jacq, Frédéric Devaux
Genome Biol. 2008; 9(11): R164. Published online 2008 November 24. doi: 10.1186/gb-2008-9-11-r164
PMCID:
PMC2614496
Abstract Full Text PDF–1.5M Supplementary Material
Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations
Valérie de Crécy-Lagard, Basma El Yacoubi, Rocío Díaz de la Garza, Alexandre Noiriel, Andrew D Hanson
BMC Genomics. 2007; 8: 245. Published online 2007 July 23. doi: 10.1186/1471-2164-8-245
PMCID:
PMC1971073
Abstract Full Text PDF–664K Supplementary Material
Structure-based activity prediction for an enzyme of unknown function
Johannes C. Hermann, Ricardo Marti-Arbona, Alexander A. Fedorov, Elena Fedorov, Steven C. Almo, Brian K. Shoichet, Frank M. Raushel
Nature. Author manuscript; available in PMC 2008 August 16.
Published in final edited form as: Nature. 2007 August 16; 448(7155): 775–779. Published online 2007 July 1. doi: 10.1038/nature05981
PMCID:
PMC2254328
Abstract Full Text PDF–1.1M Supplementary Material
CORRIE: enzyme sequence annotation with confidence estimates
Benjamin Audit, Emmanuel D Levy, Wally R Gilks, Leon Goldovsky, Christos A Ouzounis
BMC Bioinformatics. 2007; 8(Suppl 4): S3. Published online 2007 May 22. doi: 10.1186/1471-2105-8-S4-S3
PMCID:
PMC1892082
Abstract Full Text PDF–412K
High precision multi-genome scale reannotation of enzyme function by EFICAz
Adrian K Arakaki, Weidong Tian, Jeffrey Skolnick
BMC Genomics. 2006; 7: 315. Published online 2006 December 13. doi: 10.1186/1471-2164-7-315
PMCID:
PMC1764738
Abstract Full Text PDF–464K Supplementary Material
The relationship between protein sequences and their gene ontology functions
Zhong-Hui Duan, Brent Hughes, Lothar Reichel, Dianne M Perez, Ting Shi
BMC Bioinformatics. 2006; 7(Suppl 4): S11. Published online 2006 December 12. doi: 10.1186/1471-2105-7-S4-S11
PMCID:
PMC1780109
Abstract Full Text PDF–316K Supplementary Material
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification
Nandini Krishnamurthy, Duncan P Brown, Dan Kirshner, Kimmen Sjölander
Genome Biol. 2006; 7(9): R83. Published online 2006 September 14. doi: 10.1186/gb-2006-7-9-r83
PMCID:
PMC1794543
Abstract Full Text PDF–2.4M Supplementary Material
Genome comparison using Gene Ontology (GO) with statistical testing
Zhaotao Cai, Xizeng Mao, Songgang Li, Liping Wei
BMC Bioinformatics. 2006; 7: 374. Published online 2006 August 11. doi: 10.1186/1471-2105-7-374
PMCID:
PMC1569881
Abstract Full Text PDF–385K Supplementary Material
Probabilistic annotation of protein sequences based on functional classifications
Emmanuel D Levy, Christos A Ouzounis, Walter R Gilks, Benjamin Audit
BMC Bioinformatics. 2005; 6: 302. Published online 2005 December 14. doi: 10.1186/1471-2105-6-302
PMCID:
PMC1361783
Abstract Full Text PDF–465K Supplementary Material
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
David MA Martin, Matthew Berriman, Geoffrey J Barton
BMC Bioinformatics. 2004; 5: 178. Published online 2004 November 18. doi: 10.1186/1471-2105-5-178
PMCID:
PMC535938
Abstract Full Text PDF–457K Supplementary Material
Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase
Daniil G Naumoff, Ying Xu, Nicolas Glansdorff, Bernard Labedan
BMC Genomics. 2004; 5: 52. Published online 2004 August 2. doi: 10.1186/1471-2164-5-52
PMCID:
PMC514541
Abstract Full Text PDF–310K
Cross-species comparison of genome-wide expression patterns
Xianghong Jasmine Zhou, Greg Gibson
Genome Biol. 2004; 5(7): 232. Published online 2004 June 21. doi: 10.1186/gb-2004-5-7-232
PMCID:
PMC463279
Abstract Full Text PDF–84K
JEvTrace: refinement and variations of the evolutionary trace in JAVA
Marcin P Joachimiak, Fred E Cohen
Genome Biol. 2002; 3(12): research0077.1–research0077.12. Published online 2002 November 26.
PMCID:
PMC151179
Abstract Full Text PDF–949K
Orthologs and paralogs - we need to get it right
Roy A Jensen
Genome Biol. 2001; 2(8): interactions1002.1–interactions1002.3. Published online 2001 August 3.
PMCID:
PMC138949
Abstract Full Text PDF–74K
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